Contacts of the helix formed by residues 726 - 738 (chain A) in PDB entry 2HWK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 726 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ASN* 5.0 0.9 - - - +
604A ARG* 3.3 8.7 + - - +
690A TYR* 3.5 24.9 - - + +
693A CYS* 3.3 6.2 - - - +
694A GLU* 3.3 44.4 + - + +
697A ALA* 3.8 3.6 - - - +
724A TYR 3.4 1.9 - - - +
725A ALA* 1.3 77.1 - - - +
727A ARG* 1.3 64.2 + - - +
728A ALA* 3.2 11.7 + - - +
729A SER* 2.9 42.2 + - - -
730A GLU 3.2 17.8 + - - -
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Residues in contact with ARG 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A GLU* 4.6 14.1 + - - +
514A ILE* 6.0 0.2 - - - +
517A ASN* 3.4 30.9 + - - +
527A ASP* 4.2 7.2 - - - +
528A LEU* 3.6 35.3 - - - +
529A ASP* 3.3 36.4 + - - +
556A TYR* 5.4 3.0 + - - -
604A ARG* 3.5 28.7 - - - +
690A TYR* 4.8 0.6 + - - -
726A ASP* 1.3 72.5 - - - +
728A ALA* 1.3 69.7 + - + +
730A GLU* 3.5 3.2 + - - +
731A SER* 3.0 23.9 + - - -
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Residues in contact with ALA 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A ILE* 4.1 33.4 - - + -
694A GLU* 6.2 0.4 - - + +
697A ALA* 4.2 6.1 - - + -
726A ASP* 3.2 8.8 + - - +
727A ARG* 1.3 84.1 - - + +
729A SER* 1.3 54.7 + - - +
731A SER* 3.0 7.5 + - - -
732A ILE* 2.8 44.9 + - + +
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Residues in contact with SER 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A CYS* 3.7 6.8 + - - -
697A ALA* 3.4 13.7 - - - +
700A LEU* 3.8 22.4 - - - +
723A GLY 4.1 2.0 - - - -
724A TYR* 3.5 20.6 - - - -
726A ASP* 2.9 33.6 + - - -
728A ALA* 1.3 74.8 - - - +
730A GLU* 1.3 60.1 + - - +
732A ILE* 3.3 4.5 + - - +
733A ILE* 2.9 36.2 + - - +
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Residues in contact with GLU 730 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604A ARG* 2.8 35.3 + - - +
605A ARG 5.6 0.2 - - - +
607A PRO* 4.0 21.3 - - - +
724A TYR* 3.3 27.5 - - + +
726A ASP 3.2 13.8 + - - +
727A ARG* 3.7 4.3 - - - +
729A SER* 1.3 79.6 - - - +
731A SER* 1.3 60.1 + - - +
733A ILE* 4.2 0.9 - - - +
734A GLY* 3.2 19.8 + - - -
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Residues in contact with SER 731 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A ARG 3.0 14.5 + - - -
728A ALA* 3.3 10.3 - - - -
730A GLU* 1.3 78.3 - - - +
732A ILE* 1.3 58.2 + - - +
734A GLY* 3.4 2.0 + - - -
735A ALA* 3.0 28.8 + - - +
738A ARG* 5.0 2.4 + - - -
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Residues in contact with ILE 732 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A ILE* 5.4 2.5 - - + -
697A ALA 3.7 13.7 - - - +
700A LEU* 3.8 31.4 - - + +
701A SER* 3.6 27.1 - - - +
705A LYS* 4.2 16.8 - - + +
728A ALA* 2.8 37.8 + - + +
729A SER* 3.7 5.8 - - - +
731A SER* 1.3 70.6 - - - +
733A ILE* 1.3 60.3 + - - +
735A ALA* 3.2 8.3 + - - +
736A ILE* 3.0 45.8 + - + +
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Residues in contact with ILE 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A LEU* 4.1 22.9 - - + -
704A THR* 5.7 0.9 - - + -
724A TYR* 4.0 35.4 - - + -
729A SER 2.9 24.9 + - - +
730A GLU 4.3 1.3 - - - +
732A ILE* 1.3 72.7 - - - +
734A GLY* 1.3 52.9 + - - +
736A ILE* 3.4 10.2 + - + +
737A ALA* 2.7 34.6 + - + +
759A PHE* 4.0 35.7 - - + -
761A PHE* 4.3 19.0 - - + -
776A LEU* 4.4 15.9 - - + -
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Residues in contact with GLY 734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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730A GLU 3.2 13.6 + - - -
731A SER 3.8 2.7 - - - -
732A ILE 3.2 0.2 - - - -
733A ILE* 1.3 78.9 - - - +
735A ALA* 1.3 63.0 + - - +
737A ALA* 4.0 5.5 - - - +
738A ARG* 3.1 43.1 + - - +
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Residues in contact with ALA 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A LYS* 4.5 22.7 - - - +
731A SER 3.0 15.0 + - - +
732A ILE* 3.4 11.9 - - - +
734A GLY* 1.3 77.9 - - - +
736A ILE* 1.3 60.4 + - - +
738A ARG* 3.2 32.3 + - - +
739A GLN* 3.6 13.0 - - - +
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Residues in contact with ILE 736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A LEU* 5.7 0.2 - - + -
704A THR* 3.6 29.6 - - + +
705A LYS* 3.8 31.0 - - + +
708A CYS* 3.9 13.7 - - - -
717A CYS* 5.6 0.7 - - + -
732A ILE* 3.0 28.8 + - + +
733A ILE* 3.7 10.5 - - + +
735A ALA* 1.3 72.8 - - - +
737A ALA* 1.3 65.3 + - - +
738A ARG 3.2 1.8 - - - -
739A GLN* 3.1 16.4 + - - +
740A PHE* 3.1 30.2 - - + -
761A PHE* 3.5 33.4 - - + -
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Residues in contact with ALA 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A ILE* 2.7 22.5 + - + +
734A GLY* 4.0 5.8 - - - +
736A ILE* 1.3 72.9 - - - +
738A ARG* 1.3 59.2 + - + +
739A GLN 2.9 6.5 + - - -
740A PHE 3.3 15.2 + - - +
743A SER* 3.4 31.4 + - - +
761A PHE* 3.7 13.9 - - + -
772A ASN* 5.1 9.9 - - - +
776A LEU* 4.7 9.0 - - + -
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Residues in contact with ARG 738 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A SER 5.0 2.4 + - - -
734A GLY* 3.1 31.2 + - - +
735A ALA* 3.2 32.8 - - - +
736A ILE 3.2 1.2 - - - -
737A ALA* 1.3 75.9 - - - +
739A GLN* 1.3 67.7 + - - +
740A PHE 3.6 2.0 - - - -
766A ARG* 5.3 0.3 - - - -
767A LYS 4.4 13.0 - - - +
768A ALA* 5.8 0.7 - - - -
769A ARG* 5.2 7.8 + - + +
771A HIS* 5.7 7.3 - - - -
772A ASN* 6.0 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il